Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time


Last modified by puchades on 2022/11/02 10:16
From version 26.1
edited by sharoncy
on 2020/03/09 14:37
Change comment: There is no comment for this version
To version 31.1
edited by puchades
on 2020/03/12 16:55
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.sharoncy
1 +XWiki.puchades
Content
... ... @@ -1,28 +1,52 @@
1 -(% class="jumbotron" %)
2 -(((
3 -(% class="container" %)
4 -(((
5 -== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
1 +(% style="text-align:center" %)
2 +[[image:QUINT_workflow_pic.png]]
6 6  
7 -(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
8 -)))
9 -)))
4 +== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
10 10  
11 -==== ====
12 -
13 -
14 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
15 -
16 16  The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software:
17 17  
18 18  1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
19 19  1. [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections.
20 -1. (% style="color:#2980b9" %)//Nutil//(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of ilastik and QuickNII.
10 +1. (% style="color:#2980b9" %)Nutil(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of ilastik and QuickNII.
21 21  
22 22  In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.
23 23  
14 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
15 +
16 +
17 +
18 +
19 +
20 +
21 +
22 +
23 +
24 24  [[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
25 25  
26 +(% class="wikigeneratedid" %)
27 +==== ====
28 +
29 +(% class="wikigeneratedid" %)
30 +==== ====
31 +
32 +(% class="wikigeneratedid" %)
33 +==== ====
34 +
35 +(% class="wikigeneratedid" %)
36 +==== ====
37 +
38 +(% class="wikigeneratedid" %)
39 +==== ====
40 +
41 +(% class="wikigeneratedid" %)
42 +==== ====
43 +
44 +(% class="wikigeneratedid" %)
45 +==== ====
46 +
47 +(% class="wikigeneratedid" %)
48 +==== ====
49 +
26 26  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
27 27  
28 28  * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
QUINT_workflow_pic.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +252.6 KB
Content
Youtube_QUINT.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +1.1 MB
Content